Hello, This reflects a difference in the methodology used to generate the data. Compare the two using information from each track's description page to understand the contents. The major difference appears to be in the criteria for calling and volume of predicted/non-coding transcripts (& genes). Between the two, RefGene is more current (Data last updated: 2009-07-15) than Ensembl (Data last updated: 2008-03-03). RefSeq is updated by our daily GenBank BLAT processes and Ensembl is updated once per each major release. Ensembl Release 55 (14 July 2009) was just made available and is not part of galGal3.
We hope this helps, Jennifer Jackson UCSC Genome Bioinformatics Group ----- Original Message ----- From: Hua Li <[email protected]> To: '[email protected]' <[email protected]> Sent: Wed, 15 Jul 2009 14:54:00 -0700 (PDT) Subject: [Genome] Chicken RefFlat.txt file I found that there are about 4400 chicken genes in the refFlat table, while there are about 15,000 chicken genes from Ensembl. I wonder why there is such a big difference here. Thanks, Hua Li Stowers Institue for Medical Research _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
